From E.A.Moore@open.ac.uk Wed Dec 9 10:57:43 1992 Message-Id: <199212091315.AA00566@oscsunb.ccl.net> Date: Wed, 9 Dec 1992 10:57:43 +0000 From: E.A.Moore@open.ac.uk To: CHEMISTRY@ccl.net Subject: surface charges/distance course on MD etc Dear netters, 1. The only reply I had to my query about surface charges was from someone wanting to know the answer. Is there no-one out there who can tell me how to estimate the charge of an ion on a surface. I have tried various surface and solid state books and come away with the impression that the ions at the surface have very low charges, but I need to know how large; is 0.6 reasonable or is it really low like 0.1? Would programs like CRYSTAL tell me? 2.For my second question I would greatly appreciate responses from European subscribers in particular. It seems to me that molecular dynamics and similar programs are increasingly being used by organic chemists and pharmacy graduates Indeed I recently attended a presentation in which the package was designed to be used by benchtop chemists rather than theoreticians. Does anyone think there might be a market for a post experience (aimed at people working in industry) course which would discuss the basis of molecular dynamics type programs and how far results from them are reliable ? When are the results good enough for the experimenters purposes and when should they be treated with caution. Are the programs already sufficiently documented? Is all the relevant information available from readily accessible books? Elaine A. Moore Chemistry Dept., The Open University, Milton Keynes MK7 6AA UK E.A.Moore@UK.AC.OPEN From shen@athena.cs.uga.edu Tue Dec 8 20:44:32 1992 Date: Wed, 9 Dec 92 01:44:32 EST From: Mingzuo Shen Message-Id: <9212090644.AA14676@athena.cs.uga.edu> To: chemistry@ccl.net Subject: finite differences of energy gradients with symmetry Hi all, I wonder if someone has such a program already and would like to share it, that calculates energy second derivatives from energy gradients via finite differences, and that takes into account of ANY point group (not just the nondegenerate ones). For example consider the benzene molecule, D6h. Consider a particular hydrogen nucleus. If a program really uses the D6h symmetry, then we need only to displace the hydrogen nucleus along the positive and negative x-axis, positive and negative y-axis, and positive z-axis (molecule on the xy-plane). Then the partial derivatives of the energy with respect to all hydrogen nuclei should be calculable from symmetry. Similarly for the carbon atoms. Thus a total of 10 displacements would be needed. If we only use the D2h subgroup, 20 displacements would be needed, doubling the computational cost while losing numerical precision, which does not exactly looks like a smart thing to do. The saving is even more substantial if we consider the tropylium ion (C7H7+, D7h, whose abelian subgroup is only C2v). Recently I was contemplating the planar [7]circulene (seven benzene rings fused together, D7h) and was discouraged from using the C2v subgroup. Let's not mention C60. I think such a program could be widely welcome, no? Any pointer and/or help is appreciated. Mingzuo Shen From ivan@gandalf.ciam.unibo.it Wed Dec 9 17:05:45 1992 Date: Wed, 9 Dec 1992 16:05:45 +0100 From: ivan@gandalf.ciam.unibo.it (Ivan Rossi) Message-Id: <9212091505.AA14571@gandalf.ciam.unibo.it> To: chemistry@ccl.net Subject: Z-matrix generators Dear netters, I know that this is probably a FAQ, but i'm new to the CCL. Does anyone know about some public domain/shareware/cheap graphical molecular builder which could create Z-matrix? I need a sort of Z- matrix editor to use as a crude input interface to Gaussian I use a RS/6000 workstation. Thanks in advance Ivan Rossi | Department of Chemistry "G.Ciamician" | REACTIVITY University of Bologna - Italy | Nothing less and nothing more e-mail: ivan@gandalf.ciam.unibo.it | From BOYD_DONALD_B@INET.D48.LILLY.COM Sun Dec 9 05:18:03 1992 Date: 09 Dec 1992 10:18:03 -0500 (EST) From: "DONALD B. BOYD" Subject: Reviews in Computational Chemistry To: chemistry@ccl.net Message-Id: <01GS3WTQS64I8WVZI2@INET.D48.LILLY.COM> In response to a request that it would be helpful to have an on-line version of the contents of the book series REVIEWS IN COMPUTATIONAL CHEMISTRY, the following is provided. Authors of Volume 1 (1990): David Feller and Ernest R. Davidson, Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions. James J. P. Stewart, Semiempirical Molecular Orbital Methods. Clifford E. Dykstra, Joseph D. Augspurger, Bernard Kirtman, and David J. Malik, Properties of Molecules by Direct Calculation. Ernest L. Plummer, The Application of Quantitative Design Strategies in Pesticide Design. Peter C. Jurs, Chemometrics and Multivariate Analysis in Analytical Chemistry. Yvonne C. Martin, Mark G. Bures, and Peter Willett, Searching Databases of Three-Dimensional Structures. Paul G. Mezey, Molecular Surfaces. Terry P. Lybrand, Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods. Donald B. Boyd, Aspects of Molecular Modeling. Donald B. Boyd, Successes of Computer-Assisted Molecular Design. Ernest R. Davidson, Perspectives on Ab Initio Calculations. Authors of Volume 2 (1991): Andrew R. Leach, A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. John M. Troyer and Fred E. Cohen, Simplified Models for Understanding and Predicting Protein Structure. J. Phillip Bowen and Norman L. Allinger, Molecular Mechanics: The Art and Science of Parameterization. Uri Dinur and Arnold T. Hagler, New Approaches to Empirical Force Fields. Steve Scheiner, Calculating the Properties of Hydrogen Bonds by Ab Initio Methods. Donald E. Williams, Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential. Peter Politzer and Jane S. Murray, Molecular Electrostatic Potentials and Chemical Reactivity. Michael C. Zerner, Semiempirical Molecular Orbital Methods. Lowell H. Hall and Lemont B. Kier, The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling. I. B. Bersuker and A. S. Dimoglo, The Electron-Topological Approach to the QSAR Problem. Donald B. Boyd, The Computational Chemistry Literature. Authors of Volume 3 (1992): Tamar Schlick, Optimization Methods in Computational Chemistry. Harold A. Scheraga, Predicting Three-Dimensional Structures of Oligopeptides. Andrew E. Torda and Wilfred F. van Gunsteren, Molecular Modeling Using NMR Data. David F. V. Lewis, Computer-Assisted Methods in the Evaluation of Chemical Toxicity. In addition, each volume contains a Compendium of Molecular Modeling Software. REVIEWS IN COMPUTATIONAL CHEMISTRY is published by VCH and is edited by K. B. Lipkowitz and Donald B. Boyd. From: BOYD DONALD B (MCVAX0::QSAR) To: VMS MAIL ADDRESSEE (INT::"chemistry@ccl.net") cc: BOYD DONALD B (MCVAX0::QSAR) From rafapa@obelix.cica.es Wed Dec 9 18:35:08 1992 Date: Wed, 9 Dec 1992 18:35:08 UTC+0100 From: rafapa@obelix.cica.es Subject: Newzmat: from xyz to z-matrix To: chemistry@ccl.net, rafapa@esevvx.cica.es Message-Id: <9212091735.AA05261@obelix.cica.es> >X-Envelope-to: chemistry@ccl.net I am trying to convert from cartesian coordinates to z-matrix format suitable for Gaussian92 using the newzmat program. I want to have a few dummy atoms in the final z-matrix so I have been trying to use the -tzmat option to give a template z-matrix. Whatever I try the program always finish with an Link1 error message. Somebody knows if the use of dummy atoms is not possible in the template z-matrix? thanks in advance Dr. Rafael R. Pappalardo Dept. Physical Chemistry Univ. de Sevilla (SPAIN) e-mail:rafapa@obelix.cica.es From dchin%emperor@harvard.harvard.edu Wed Dec 9 08:05:34 1992 Date: Wed, 9 Dec 92 13:05:34 -0500 From: dchin%emperor@harvard.harvard.edu (Donovan Chin) Message-Id: <9212091805.AA06536@emperor.harvard.edu> To: chemistry@ccl.net Subject: Fortran buffs.. Greetings, I have a question related to fortran (for comp. chem. code). I want to write a file in 'matrix format'. ie , an output for a 3x3 matrix: a b c d e f g h i The existing code simply is: do i=1, a write(*,200) (tor(i,j), j=1, a) 200 format(3(1x,f10.4,',')) enddo Where 'a' in this case is 3 and is user defined (for different sizes). The question is about the format statement '200' I have to set the size '3' then compile. Fortran wont let me use a variable (in this case 'a') in the format statement. The question, is there a work around to make the format statement variable and reflect the dimension of the matrix without re-editing and re-compiling? Any suggestions for a novice? Thanks ahead of time, Donovan =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-= Donovan Chin Ph.d Phone: 617.496.6820 Fax: 617.495.9857 Harvard University e-mail dchin@emperor.harvard.edu Department of Chemistry 12 Oxford St. Cambridge, MA 02138, USA =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-= From orgk2-a.sundin@macpost.lu.se Wed Dec 9 20:24:11 1992 Subject: Input structure to AM1 To: CHEMISTRY@ccl.net From: Anders.Sundin@orgk2.lth.se Date: Wed, 9 Dec 92 19:24:11 +0100 Message-Id: <921209.192411.1254@macpost.lu.se> Dear netters, I have a question about structures used as input to semi-empirical (or ab initio programs). Is it more correct to do a (usually "better") MM2 energy minimization than to do an AM1 energy minimization on a structure before calculating its semi-empirical (AM1) properties? In my case the coordinates of the energy minimized flavones from AM1 and MM2 were very similar, superimposition gave an RMS of fit of 0.076 A. Thanks! -- Anders Sundin e-mail: Anders.Sundin@orgk2.lth.se Organic Chemistry 2 sundinKC@dna.lth.se Lund University ok2aps@seldc52.bitnet P.O. Box 124 voice: +46 46 104130 S-22100 Lund, Sweden fax: +46 46 108209 From mes@ATLAS.CHEMISTRY.UAKRON.EDU Wed Dec 9 08:28:38 1992 Date: Wed, 9 Dec 92 13:28:38 EST From: mes@atlas.chemistry.uakron.edu (mary ellen scott) To: chemistry@ccl.net Subject: MOPAC Message-Id: Is anyone working with "simple sugars" and doing geometry optimizations? I am looking for a literature value for the heat of formation of Glucose. The Quanta/Mopac interface give -266kcal/mole. I am not sure that mopac is actually reading the imput file from quanta correctly. I cannot find the proper # of bonds in the output and the C1-O5 bond is not defined in z-matrix. If anyone is familiar with some references on MO calculations for glucose that would be great. And If anyone is working with the quanta/mopac interface- lets talk. Thanks in advance. Mary Ellen From schw0531@compszrz.zrz.tu-berlin.de Wed Dec 9 20:36:15 1992 Date: Wed, 9 Dec 92 19:36:15 +0100 From: Prof. Dr. Helmut Schwarz Message-Id: <9212091836.AA18516@compszrz.zrz.tu-berlin.de> To: CHEMISTRY@ccl.net Subject: conferences Some time ago I had a question about a file or data base with conferences and symposia on the object Quantum/comp. Chem. >From the response I have until now it seems that such file Jan Hrusak schw0531@compszrz.zrz.tu-berlin.de From sam@ncsa.uiuc.edu Wed Dec 9 06:44:39 1992 Date: Wed, 9 Dec 92 12:44:39 CST From: sam@ncsa.uiuc.edu (Sam Milosevich) Message-Id: <9212091844.AA27419@troon.ncsa.uiuc.edu> To: CHEMISTRY@ccl.net Subject: symposium on computer-enhanced analytical spectroscopy ? Howdy! We read the posting to the CHEMISTRY@ccl.net mailing list about the 4th "symposium on computer-enhanced analytical spectroscopy" which was held in Salt Lake City in June. Can anyone tell us about the possibility and location of the meeting in '93? Thanks! ---Sam * Phone: +1-317-276-9118; FAX: +1-317-276-5431 (attn: Sam) * * E-mail: sam@ncsa.uiuc.edu (NCSA Partners), sam@lilly.com * * X.400: G=Samuel; S=Milosevich; P=Lilly; A=ATTmail; C=US; * From wei@hermes.chpc.utexas.edu Wed Dec 9 10:32:07 1992 Date: Wed, 9 Dec 1992 16:32:07 -0600 From: wei@hermes.chpc.utexas.edu Message-Id: <9212092232.AA23255@methyl> To: chemistry@ccl.net, dchin%emperor@harvard.harvard.edu Subject: Re: Fortran buffs.. The following simple program will write a matrix for n <= 10. program main parameter (n=5) dimension a(10,10) do 1 j = 1, n do 1 i = 1, n a(i,j) = i * j 1 continue do 2 i = 1, n 2 write(5,123) (a(i,j),j=1,n) 123 format(10(f8.3)) stop end You need to give a maximum number of columns, it is 10 here. Hope it helps. Tai-Guang Wei From rpm@wag.caltech.edu Wed Dec 9 06:46:14 1992 Date: Wed, 9 Dec 1992 14:46:14 -0800 From: "Richard P. Muller" Message-Id: <199212092246.AA08640@bach.wag.caltech.edu> To: chemistry@ccl.net Subject: Where to find ZNDO program? Where can I find M Zerner's ZNDO program? Is it distributed through QCPE? Is it available via anonymous ftp? I apologize if this is a FAQ, but I checked the past year's postings and could find no obvious leads. Any help given will be greatly appreciated. Rick Muller rpm@wag.caltech.edu From doherty@msc.edu Wed Dec 9 11:06:42 1992 Message-Id: <9212092306.AA07380@uh.msc.edu> Date: Wed, 9 Dec 1992 17:06:42 -0600 To: dchin%emperor@harvard.harvard.edu (Donovan Chin) From: doherty@msc.edu (David C. Doherty) Subject: Re: Fortran buffs.. Donovan Chin writes: >Greetings, >I have a question related to fortran (for comp. chem. code). > >I want to write a file in 'matrix format'. > >... > >in the format statement. The question, is there a work around to >make the format statement variable and reflect the dimension of the >matrix without re-editing and re-compiling? > >Any suggestions for a novice? In a didactic mood, I am posting this to the list rather than just to the original poster. May it enlighten others as well ;-). VAX FORTRAN allows the use of in the format specifier, where n is an integer. (This is not f77 compliant) A more standard f77 approach involves two (somewhat) esoteric concepts in fortran: runtime formats and internal writes. The approach is to construct the format statement on-the-fly, by writing it to a character variable using an internal write. The following code and its output illustrates such. the code: --- program FmtTest c c snippet to test an internal write to a format string c integer m,n parameter (m=4,n=3) real tor(4,3) c character variable to store the format string character*80 fmt c data tor / 1.0, 2.0, 3.0, 4.0, 1 5.0, 6.0, 7.0, 8.0, 2 9.0, 10.0, 11.0, 12.0 / c c create a runtime format by doing an internal write to c the format variable, fmt c write(fmt,100)'(',m,'(1x,f10.4))' 100 format(a,i3,a) c output the format for giggles write(6,'(a)')fmt c do i=1,n c c use the runtime format in the write statement c write(6,fmt) (tor(j,i), j=1, m) enddo c end --- the output: --- [sf:/wrk/doherty]> cf77 -o FmtTest FmtTest.f [sf:/wrk/doherty]> FmtTest ( 4(1x,f10.4)) 1.0000 2.0000 3.0000 4.0000 5.0000 6.0000 7.0000 8.0000 9.0000 10.0000 11.0000 12.0000 --- Dave Doherty --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From shepard@dirac.tcg.anl.gov Wed Dec 9 11:15:50 1992 Date: Wed, 9 Dec 92 17:15:50 CST From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9212092315.AA13555@dirac.tcg.anl.gov> To: chemistry@ccl.net Subject: Printing large arrays in Fortran dchin@emperor.harvard.edu writes: >[deleted text] > do i=1, a > write(*,200) (tor(i,j), j=1, a) > 200 format(3(1x,f10.4,',')) > enddo >[deleted text] >The question, is there a work around to >make the format statement variable and reflect the dimension of the >matrix without re-editing and re-compiling? The easiest thing to do is simply to replace the 3 with a larger number. 200 format(10(1x,f10.4,',')) This will work as you want it to until a>10, and then things will start looking funny. If you want to print out larger arrays in a readable format, you have to go to a little bit more effort. The following is one of several similar routines for printing real*8 floating point arrays that is used in the COLUMBUS Program System. In your example, it would be called as call prblk( tor, a, a, a, 0, 0, 'row', 'col', 1, 6 ) assuming unit 6 is the standard output. This routine (along with its partners, some of which have simpler calling sequences), is found in the colib3.f file of library routines in COLUMBUS. Regards, -ron shepard ********************************************************************** *deck prblk subroutine prblk( & z, nrd, nr, nc, r0, c0, labr, labc, ifmt, nlist ) c c print a sub-block of a rectangular matrix. c this version prints eight columns at a time with three formats. c parameter ncol and formats 10 and 1-3 should be modified to print c a different number of columns or to use different formats. c c input: c z(*) = matrix to be printed. c nrd = row dimension. c nr = number of rows to print. c nc = column dimension. c r0 = row number offset. c c0 = column number offset. c labr = character row label. c labc = character column label. c ifmt = format type (1:f, 2:e, 3:g). c nlist= output unit number. c c format statement assignment version 5-jun-87 (rls). c ron shepard 17-may-84. c implicit logical(a-z) c integer nrd, nr, nc, r0, c0, ifmt, nlist character*(*) labr,labc real*8 z(nrd,nc) c integer ncol parameter (ncol=8) 10 format(/8x,8(6x,a4,i4,1x)) 1 format(1x,a4,i4,8f15.8) 2 format(1x,a4,i4,1p,8e15.6) 3 format(1x,a4,i4,1p,8g15.6) c integer fmtz, i, ilab, j, jlab1, jlab2, jlast, jstrt, jt c real*8 zero parameter (zero=0d0) c if(ifmt.le.1)then assign 1 to fmtz elseif(ifmt.eq.2)then assign 2 to fmtz else assign 3 to fmtz endif c jlast=0 do 400 jstrt=1,nc,ncol jlast=min(nc,jlast+ncol) c jlab1=jstrt+c0 jlab2=jlast+c0 write(nlist,10)(labc,j,j=jlab1,jlab2) c do 300 i=1,nr ilab=i+r0 c c print the row if a nonzero element is found. c do 100 j=jstrt,jlast if(z(i,j).ne.zero)then write(nlist,fmtz)labr,ilab,(z(i,jt),jt=jstrt,jlast) go to 300 endif 100 continue 300 continue 400 continue c return end From jk@iris68.biosym.com Wed Dec 9 08:28:30 1992 Date: Wed, 9 Dec 92 16:28:30 -0800 From: jk@iris68.biosym.com (Kottalam) Message-Id: <9212100028.AA17380@iris68.biosym.com> To: chemistry@ccl.net Subject: RE: fortran buffs The following program illustrates how to edit I/O formats at run time. It ran correctly on an Iris workstation. As far as I know it conforms to ANSI FORTRAN 77 standard. ----------------------------------------------------- program test parameter (M=10) c real tor(M,M) character*20 form data form /'(??(1x,f10.4,'',''))'/ c read (*,*) n c********************************************* write (form(2:3),'(i2)') n C THIS IS CALLED I/O TO "INTERNAL FILES" c********************************************* write (*,*) 'Will use the format:', form c do 20 i = 1,n do 10 j = 1,n tor(i,j) = float(i+j) 10 continue 20 continue c do 30 i = 1,n write (*,form) (tor(i,j),j=1,n) 30 continue c end ----------------------------------------------------- Kottalam jk@biosym.com (619) 546 5366 \ | / - O - Scientists are objective; / | \ The Earth sucks and they call it gravity.